Methods and processes for non-invasive assessment of genetic variations

Abstract

Provided herein are methods, processes, systems and apparatuses for non-invasive assessment of a chromosome aneuploidy in a fetus according to a comparison of ratios of counts of sequence reads mapped to certain chromosomes. Also provided herein are methods, processes, systems and apparatuses for non-invasive assessment of a copy number variation in a fetus.

What is claimed is: 
     
       1. A computer-implemented method for outputting a classification of presence or absence of a chromosome aneuploidy for sequenced test sample nucleic acid from a pregnant female, comprising:
 (a) sequencing test sample nucleic acid by a massively parallel sequencer that generates sequence reads, which test sample nucleic acid comprises circulating cell-free nucleic acid from blood of a pregnant female bearing a fetus, wherein the sequencing is at about 1-fold coverage or less; 
 (b) mapping, using a microprocessor, the sequence reads to portions of a reference genome; 
 (c) counting, using a microprocessor, the sequence reads mapped to the portions, which counting generates counts of sequence reads mapped to the portions; 
 (d) normalizing, using a microprocessor, the counts of sequence reads mapped to chromosomes 13, 18, and 21, or segments thereof, according to guanine-cytosine (GC) content, which normalizing generates normalized counts; 
 (e) calculating, using a microprocessor, three ratios from the normalized counts, wherein the three ratios consist of:
 (i) a ratio between counts mapped to chromosome 13, or segment thereof, to counts mapped to chromosome 21, or segment thereof, 
 (ii) a ratio between counts mapped to chromosome 13, or segment thereof, to counts mapped to chromosome 18, or segment thereof, and 
 (iii) a ratio between counts mapped to chromosome 18, or segment thereof, to counts mapped to chromosome 21, or segment thereof; 
 
 (f) computationally comparing, using a microprocessor, the three ratios to corresponding ratios of one or more euploid samples, which comparing generates a comparison; and 
 (g) outputting, using a microprocessor, a classification of the presence of absence of a chromosome aneuploidy for the test sample according to the comparison generated in (f). 
 
     
     
       2. The method of  claim 1 , wherein the nucleic acid is from blood plasma or blood serum. 
     
     
       3. The method of  claim 1 , comprising generating and transmitting a laboratory prenatal test report comprising a classification of presence or absence of three copies of a chromosome for the test sample. 
     
     
       4. The method of  claim 3 , wherein the report comprises one or more of a sensitivity, specificity and confidence interval for the classification. 
     
     
       5. The method of  claim 4 , wherein the sensitivity is 95% or greater and the specificity is 99% or greater. 
     
     
       6. The method of  claim 1 , comprising monitoring health of the fetus and pregnant female from whom the test sample was obtained based on the number of copies of a chromosome in the fetus. 
     
     
       7. The method of  claim 6 , comprising performing a medical procedure comprising amniocentesis or chorionic villus sampling when the classification is presence of three copies of a chromosome. 
     
     
       8. The method of  claim 1 , wherein the comparison is a Cartesian coordinate in three-dimensional space. 
     
     
       9. The method of  claim 1 , wherein the comparing in (f) comprises plotting the three ratios calculated in (e) in three dimensions, which dimensions are the ratios, and the comparison is a point for the subject on a three dimensional plot. 
     
     
       10. The method of  claim 9 , wherein the outputting the classification in (g) comprises calculating the distance between the point for the subject to a point or points for the one or more euploid samples. 
     
     
       11. The method of  claim 1 , wherein the sequencing is by a genome-wide massively parallel sequencer. 
     
     
       12. The method of  claim 1 , wherein the comparison generated in (f) is not based on segments of the genome other than in chromosomes 13, 18 and 21.